Influence of protein charge patches on the structure of protein-polyelectrolyte complexes

Form Equals Function: Influence of Coacervate Architecture on Drug Delivery Applications

Complex coacervates, formed through electrostatic interactions between oppositely charged polymers, present a versatile platform for drug delivery, providing rapid assembly, selective encapsulation, and responsiveness to environmental stimuli. The architecture and properties of coacervates can be tuned by controlling structural and environmental design factors, which significantly impact the stability and delivery efficiency of the drugs. While environmental design factors such as salt, pH, and temperature play a crucial role in coacervate formation, structural design factors such as polymer concentration, polymer structure, mixing ratio, and chain length serve as the core framework that shapes coacervate architecture. These elements modulate the phase behavior and material properties of coacervates, allowing for a highly tunable system. In this review, we primarily analyze how these structural design factors contribute to the formation of diverse coacervate architecture, ranging from bulk coacervates to polyion complex micelles, vesicles, and cross-linked gels, though environmental design factors are considered. We then examine the effectiveness of these architectures in enhancing the delivery and efficacy of drugs across various administration routes, such as noninvasive (e.g., oral and transdermal) and invasive delivery. This review aims to provide foundational insights into the design of advanced drug delivery systems by examining how the origin and chemical structure of polymers influence coacervate architecture, which in turn defines their material properties. We then explore how the architecture can be tailored to optimize drug delivery for specific administration routes. This approach leverages the intrinsic properties derived from the coacervate architecture to enable targeted, controlled, and efficient drug release, ultimately enhancing therapeutic outcomes in precision medicine.

Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning

Protein-DNA interactions and protein-mediated DNA compaction play key roles in a range of biological processes. The length scales typically involved in DNA bending, bridging, looping, and compaction (≥1 kbp) are challenging to address experimentally or by all-atom molecular dynamics simulations, making coarse-grained simulations a natural approach. Here, we present a simple and generic coarse-grained model for DNA-protein and protein-protein interactions and investigate the role of the latter in the protein-induced compaction of DNA. Our approach models the DNA as a discrete worm-like chain. The proteins are treated in the grand canonical ensemble, and the protein-DNA binding strength is taken from experimental measurements. Protein-DNA interactions are modeled as an isotropic binding potential with an imposed binding valency without specific assumptions about the binding geometry. To systematically and quantitatively classify DNA-protein complexes, we present an unsupervised machine learning pipeline that receives a large set of structural order parameters as input, reduces the dimensionality via principal-component analysis, and groups the results using a Gaussian mixture model. We apply our method to recent data on the compaction of viral genome-length DNA by HIV integrase and find that protein-protein interactions are critical to the formation of looped intermediate structures seen experimentally. Our methodology is broadly applicable to DNA-binding proteins and protein-induced DNA compaction and provides a systematic and semi-quantitative approach for analyzing their mesoscale complexes.

Structure and Dynamics of Hybrid Colloid-Polyelectrolyte Coacervates: Insights from Molecular Simulations

Electrostatic interactions in polymeric systems are responsible for a wide range of liquid-liquid phase transitions that are of importance for biology and materials science. Such transitions are referred to as complex coacervation, and recent studies have sought to understand the underlying physics and chemistry. Most theoretical and simulation efforts to date have focused on oppositely charged linear polyelectrolytes, which adopt nearly ideal-coil conformations in the condensed phase. However, when one of the coacervate components is a globular protein, a better model of complexation should replace one of the species with a spherical charged particle or colloid. In this work, we perform coarse-grained simulations of colloid-polyelectrolyte coacervation using a spherical model for the colloid. Simulation results indicate that the electroneutral cell of the resulting (hybrid) coacervates consists of a polyelectrolyte layer adsorbed on the colloid. Power laws for the structure and the density of the condensed phase, which are extracted from simulations, are found to be consistent with the adsorption-based scaling theory of hybrid coacervation. The coacervates remain amorphous (disordered) at a moderate colloid charge, Q, while an intra-coacervate colloidal crystal is formed above a certain threshold, at Q > Q*. In the disordered coacervate, if Q is sufficiently low, colloids diffuse as neutral nonsticky nanoparticles in the semidilute polymer solution. For higher Q, adsorption is strong and colloids become effectively sticky. Our findings are relevant for the coacervation of polyelectrolytes with proteins, spherical micelles of ionic surfactants, and solid organic or inorganic nanoparticles.

Structure and Dynamics of Hybrid Colloid-Polyelectrolyte Coacervates

We develop a scaling theory for the structure and dynamics of "hybrid" complex coacervates formed from linear polyelectrolytes (PEs) and oppositely charged spherical colloids, such as globular proteins, solid nanoparticles, or spherical micelles of ionic surfactants. At low concentrations, in stoichiometric solutions, PEs adsorb at the colloids to form electrically neutral finite-size complexes. These clusters attract each other through bridging between the adsorbed PE layers. Above a threshold concentration, macroscopic phase separation sets in. The coacervate internal structure is defined by (i) the adsorption strength and (ii) the ratio of the resulting shell thickness to the colloid radius, H/R. A scaling diagram of different coacervate regimes is constructed in terms of the colloid charge and its radius for Θ and athermal solvents. For high charges of the colloids, the shell is thick, H ≫ R, and most of the volume of the coacervate is occupied by PEs, which determine its osmotic and rheological properties. The average density of hybrid coacervates exceeds that of their PE-PE counterparts and increases with nanoparticle charge, Q. At the same time, their osmotic moduli remain equal, and the surface tension of hybrid coacervates is lower, which is a consequence of the shell's inhomogeneous density decreasing with the distance from the colloid surface. When charge correlations are weak, hybrid coacervates remain liquid and follow Rouse/reptation dynamics with a Q-dependent viscosity, η Rouse ∼ Q 4/5 and η rep ∼ Q 28/15 for a Θ solvent. For an athermal solvent, these exponents are equal to 0.89 and 2.68, respectively. The diffusion coefficients of colloids are predicted to be strongly decreasing functions of their radius and charge. Our results on how Q affects the threshold coacervation concentration and colloidal dynamics in condensed phases are consistent with experimental observations for in vitro and in vivo studies of coacervation between supercationic green fluorescent proteins (GFPs) and RNA.

Formation and physicochemical properties of glycogen phosphorylase in complex with a cationic polyelectrolyte

The accumulation of rabbit muscle glycogen phosphorylase b (RMGPb) in electrostatic complexes with the cationic polyelectrolyte poly 2-(dimethylamino) ethyl methacrylate in its quenched form (QPDMAEMA) was studied in two buffer solutions. In the N-bis(2-hydroxyethyl)-2-aminoethanesulfonic acid (BES) buffer, large complexes of RMGPb-QPDMAEMA were formed which adopted smaller sizes as QPDMAEMA concentration increased. However, in N-(2-hydroxyethyl)piperazine-N'-(2-ethanesulfonic acid) (HEPES) buffer, the hydrodynamic radius of the formed complexes gradually increased as the polymer concentration increased. Zeta potential measurements (ζ_p) showed that RMGPb significantly changed the ζ_p of the QPDMAEMA aggregates. Fluorescence studies showed that the interaction between RMGPb and QPDMAEAMA was enhanced as polymer concentration increased. Specifically, 8-anilinonaphthalene-1-sulfonic acid (ANS) fluorescence indicated that in the BES buffer the aggregates became denser as more QPDMAEMA was added, while in the HEPES buffer the density of the formed structures decreased. RMGPb's secondary structure was examined by Attenuated Total Reflection - Fourier Transform Infrared (ATR-FTIR) and Circular Dichroism (CD) showing that QPDMAEMA interaction with RMGPb does not induce any changes to the secondary structure of the enzyme. These observations suggest that cationic polyelectrolytes may be utilized for the formulation of RMGPb in multifunctional nanostructures and be further exploited in innovative biotechnology applications and bioinspired materials development.

Tuning Net Charge in Aliphatic Polycarbonates Alters Solubility and Protein Complexation Behavior

A synthetic strategy yielded polyelectrolytes and polyampholytes with tunable net charge for complexation and protein binding. Organocatalytic ring-opening polymerizations yielded aliphatic polycarbonates that were functionalized with both carboxylate and ammonium side chains in a post-polymerization, radical-mediated thiol-ene reaction. Incorporating net charge into the polymer architecture altered the chain dimensions in phosphate buffered solution in a manner consistent with self-complexation and complexation behavior with model proteins. A net cationic polyampholyte with 5% of carboxylate side chains formed large clusters rather than small complexes with bovine serum albumin, while 50% carboxylate polyampholyte was insoluble. Overall, the aliphatic polycarbonates with varying net charge exhibited different macrophase solution behaviors when mixed with protein, where self-complexation appears to compete with protein binding and larger-scale complexation.

The effects of protein charge patterning on complex coacervation

The complex coacervation of proteins with other macromolecules has applications in protein encapsulation and delivery and for determining the function of cellular coacervates. Theoretical or empirical predictions for protein coacervates would enable the design of these coacervates with tunable and predictable structure-function relationships; unfortunately, no such theories exist. To help establish predictive models, the impact of protein-specific parameters on complex coacervation were probed in this study. The complex coacervation of sequence-specific, polypeptide-tagged, GFP variants and a strong synthetic polyelectrolyte was used to evaluate the effects of protein charge patterning on phase behavior. Phase portraits for the protein coacervates demonstrated that charge patterning dictates the protein's binodal phase boundary. Protein concentrations over 100 mg mL-1 were achieved in the coacervate phase, with concentrations dependent on the tag polypeptide sequence covalently attached to the globular protein domain. In addition to shifting the binodal phase boundary, polypeptide charge patterning provided entropic advantages over isotropically patterned proteins. Together, these results show that modest changes of only a few amino acids in the tag polypeptide sequence alter the coacervation thermodynamics and can be used to tune the phase behavior of polypeptides or proteins of interest.

Direct Simulations of Phase Behavior of Mixtures of Oppositely Charged Proteins/Nanoparticles and Polyelectrolytes

We use direct simulations of particle-polyelectrolyte mixtures using the single chain in mean field framework to extract the phase diagram for such systems. At high charges of the particles and low concentration of polymers, we observe the formation of a coacervate phase involving the particles and polyelectrolytes. At low particle charges and/or high concentration of polymers, the mixture undergoes a segregative phase separation into particle-rich and polymer-rich phases, respectively. We also present results for the influence of particle charge heterogeneity on the phase diagram.

Recent progress in the science of complex coacervation

Complex coacervation is an associative, liquid-liquid phase separation that can occur in solutions of oppositely-charged macromolecular species, such as proteins, polymers, and colloids. This process results in a coacervate phase, which is a dense mix of the oppositely-charged components, and a supernatant phase, which is primarily devoid of these same species. First observed almost a century ago, coacervates have since found relevance in a wide range of applications; they are used in personal care and food products, cutting edge biotechnology, and as a motif for materials design and self-assembly. There has recently been a renaissance in our understanding of this important class of material phenomena, bringing the science of coacervation to the forefront of polymer and colloid science, biophysics, and industrial materials design. In this review, we describe the emergence of a number of these new research directions, specifically in the context of polymer-polymer complex coacervates, which are inspired by a number of key physical and chemical insights and driven by a diverse range of experimental, theoretical, and computational approaches.